[gmx-users] Is PME related to nslist??
Dear all, I am a little bit confused about electrostatic force calculation and need some clarification about PME. I normaly use PME for electrostatic force and rlist(=rcoulomb) is the parameter for real-space calculation. As you know, rlist is related NS and nstlist (the neighbor list update frequency). If I set nstlist=10, the neighbor list does not change between successive NS. Q : In the real-space calculation procedure of PME, are the particles in the neighbor list only considered?? If it is, when a new particle comes into the rlist, the PME calculation does not reflect the change until the next neighbor list update. Thanks, Joon -- Joonho Lee Department of Mechanical Science and Engineering 3213 Beckman Institute University of Illinois at Urbana-Champaign 405 N. Mathews Avenue Urbana, IL 61801 Email: lee...@uiuc.edu Phone: (217)778-9536 -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] Large dVpot/dlamda values at lambda = 1
Hi All, I'm trying to run free energy simulations for a linkage change in an oligosaccharide when bound to its protein. The linkage changes from beta 1-4 to beta 1-3. I followed the tutorial by Prof Mobley. For the lambda values I took 0 to 1 at intervals of 0.05. The values of dVpot/dlambda from 0.00 to 0.95 seem to be in the range of E3-4. But when I check the values of dVpot/dlambda for lambda = 1, it goes from E2 to E24 at the end. This is only for the LBFGS minimization. Does any one suspect a mistake in my topology or my approach? Thanks for your time. Sample .log file of lambda = 1 is pasted below. Step Time Lambda 100 100.01.0 Energies (kJ/mol) Bond AngleProper Dih. Ryckaert-Bell. LJ-14 1.06593e+048.20816e+032.93142e+024.26304e+038.30759e+03 Coulomb-14LJ (SR) Disper. corr. Coulomb (SR) Coul. recip. 4.13439e+041.92653e+05 -1.08257e+04 -1.46637e+06 -2.72128e+05 Potential Pressure (bar) dVpot/dlambda dEkin/dlambda dG/dl constr. -1.48359e+06 -4.15979e+03 -1.01327e+150.0e+000.0e+00 Step Time Lambda 101 101.01.0 Energies (kJ/mol) Bond AngleProper Dih. Ryckaert-Bell. LJ-14 1.06477e+048.21153e+032.93330e+024.26328e+038.31182e+03 Coulomb-14LJ (SR) Disper. corr. Coulomb (SR) Coul. recip. 4.13437e+041.92648e+05 -1.08257e+04 -1.49776e+06 -2.72128e+05 Potential Pressure (bar) dVpot/dlambda dEkin/dlambda dG/dl constr. -1.51500e+06 -4.33201e+03 -2.78144e+180.0e+000.0e+00 Step Time Lambda 103 103.01.0 Energies (kJ/mol) Bond AngleProper Dih. Ryckaert-Bell. LJ-14 1.06776e+048.21126e+032.93576e+024.26328e+038.31168e+03 Coulomb-14LJ (SR) Disper. corr. Coulomb (SR) Coul. recip. 4.13437e+041.92656e+05 -1.08257e+04 -1.76397e+06 -2.72128e+05 Potential Pressure (bar) dVpot/dlambda dEkin/dlambda dG/dl constr. -1.78117e+06 -5.80136e+03 -1.76071e+240.0e+000.0e+00 Regards Sai -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] Re: slow speed
; Highest order in the expansion of the constraint coupling matrix = lincs-order = 12 ; Lincs will write a warning to the stderr if in one step a bond = ; rotates over more degrees than = lincs-warnangle = 30 ; Periodic boundary conditions: xyz, no, xy pbc = xyz periodic_molecules = no ; nblist cut-off rlist= 1 ; OPTIONS FOR ELECTROSTATICS AND VDW ; Method for doing electrostatics coulombtype = Ewald rcoulomb = 1 ; Method for doing Van der Waals vdw-type = Cut-off ; cut-off lengths rvdw = 1 ; Spacing for the PME/PPPM FFT grid fourierspacing = 0.12 ; FFT grid size, when a value is 0 fourierspacing will be used fourier_nx = 0 fourier_ny = 0 fourier_nz = 0 ; EWALD/PME/PPPM parameters pme_order= 6 ewald_rtol = 1e-4 ewald_geometry = 3d epsilon_surface = 0 optimize_fft = no Can anyone help me? Thank you in advance. Thanks, Shuangxing Dai ------ next part -- An HTML attachment was scrubbed... URL: http://lists.gromacs.org/pipermail/gmx-users/attachments/20100415/73eee331/attachment-0001.html -- Message: 2 Date: Thu, 15 Apr 2010 10:09:58 -0400 From: "Justin A. Lemkul" mailto:jalem...@vt.edu>> Subject: Re: [gmx-users] slow speed To: Discussion list for GROMACS users mailto:gmx-users@gromacs.org>> Message-ID: <4bc71e36.6050...@vt.edu <mailto:4bc71e36.6050...@vt.edu>> Content-Type: text/plain; charset=UTF-8; format=flowed Shuangxing Dai wrote: > Hi, gmx-users: >I am using latest version of gromacs and found it was really slow. I > was wondering anyone got the same experience and can point out where the > problem is. >I was running double precision for MD. But for each dynamics > simulation, it takes 4 days. I should only take two or three hours. How did you establish this benchmark? Are you running in serial or in parallel? If you're running in parallel, what type of interconnect do the processors have? If they're high-latency (like gigabit ethernet) you will not get very good performance. -Justin >Here is the .mdp file: > define = > ; RUN CONTROL PARAMETERS = > integrator = sd > ; start time and timestep in ps = > tinit= 0 > dt = 0.001 > nsteps = 20 > ; number of steps for center of mass motion removal = > nstcomm = 100 > ; OUTPUT CONTROL OPTIONS = > ; Output frequency for coords (x), velocities (v) and forces (f) = > nstxout = 0 > nstvout = 0 > nstfout = 0 > ; Output frequency for energies to log file and energy file = > nstlog = 100 > nstenergy= 100 > ; Output frequency and precision for xtc file = > nstxtcout= 100 > xtc-precision= 1000 > ; NEIGHBORSEARCHING PARAMETERS = > ; nblist update frequency = > nstlist = 50 > ; ns algorithm (simple or grid) = > ns_type = grid > > ;OPTIONS FOR PRESSURE COUPLING > Pcoupl = berendsen > tau_p= 1 > compressibility = 4.5e-05 > ref_p= 0.1 > ;OPTIONS FOR TEMPERATURE COUPLING > tc_grps = system > tau_t= 0.1 > ref_t= 300 > ; OPTIONS FOR BONDS = > constraints = hbonds > ; Type of constraint algorithm = > constraint-algorithm = Lincs > ; Do not constrain the start configuration = > unconstrained-start = no > ; Relative tolerance of shake = > shake-tol= 0.0001 > ; Highest order in the expansion of the constraint coupling matrix = > lincs-order = 12 > ; Lincs will write a warning to the stderr if in one step a bond = > ; rotates over more degrees than = > lincs-warnangle = 30 > ; Periodic boundary conditions: xyz, no, xy > pbc = xyz > periodic_molecules = no > ; nblist cut-off > rlist= 1 > > ; OPTIONS FOR ELECTROSTATICS AND VDW &
[gmx-users] Re: slow speed
PPM FFT grid > fourierspacing = 0.12 > ; FFT grid size, when a value is 0 fourierspacing will be used > fourier_nx = 0 > fourier_ny = 0 > fourier_nz = 0 > ; EWALD/PME/PPPM parameters > pme_order= 6 > ewald_rtol = 1e-4 > ewald_geometry = 3d > epsilon_surface = 0 > optimize_fft = no > > Can anyone help me? Thank you in advance. > Thanks, > Shuangxing Dai > -- next part -- > An HTML attachment was scrubbed... > URL: > http://lists.gromacs.org/pipermail/gmx-users/attachments/20100415/73eee331/attachment-0001.html > > -- > > Message: 2 > Date: Thu, 15 Apr 2010 10:09:58 -0400 > From: "Justin A. Lemkul" > Subject: Re: [gmx-users] slow speed > To: Discussion list for GROMACS users > Message-ID: <4bc71e36.6050...@vt.edu> > Content-Type: text/plain; charset=UTF-8; format=flowed > > > > Shuangxing Dai wrote: > > Hi, gmx-users: > >I am using latest version of gromacs and found it was really slow. I > > was wondering anyone got the same experience and can point out where the > > problem is. > >I was running double precision for MD. But for each dynamics > > simulation, it takes 4 days. I should only take two or three hours. > > How did you establish this benchmark? Are you running in serial or in > parallel? > If you're running in parallel, what type of interconnect do the processors > have? If they're high-latency (like gigabit ethernet) you will not get > very > good performance. > > -Justin > > >Here is the .mdp file: > > define = > > ; RUN CONTROL PARAMETERS = > > integrator = sd > > ; start time and timestep in ps = > > tinit= 0 > > dt = 0.001 > > nsteps = 20 > > ; number of steps for center of mass motion removal = > > nstcomm = 100 > > ; OUTPUT CONTROL OPTIONS = > > ; Output frequency for coords (x), velocities (v) and forces (f) = > > nstxout = 0 > > nstvout = 0 > > nstfout = 0 > > ; Output frequency for energies to log file and energy file = > > nstlog = 100 > > nstenergy= 100 > > ; Output frequency and precision for xtc file = > > nstxtcout= 100 > > xtc-precision= 1000 > > ; NEIGHBORSEARCHING PARAMETERS = > > ; nblist update frequency = > > nstlist = 50 > > ; ns algorithm (simple or grid) = > > ns_type = grid > > > > ;OPTIONS FOR PRESSURE COUPLING > > Pcoupl = berendsen > > tau_p= 1 > > compressibility = 4.5e-05 > > ref_p= 0.1 > > ;OPTIONS FOR TEMPERATURE COUPLING > > tc_grps = system > > tau_t= 0.1 > > ref_t= 300 > > ; OPTIONS FOR BONDS = > > constraints = hbonds > > ; Type of constraint algorithm = > > constraint-algorithm = Lincs > > ; Do not constrain the start configuration = > > unconstrained-start = no > > ; Relative tolerance of shake = > > shake-tol= 0.0001 > > ; Highest order in the expansion of the constraint coupling matrix = > > lincs-order = 12 > > ; Lincs will write a warning to the stderr if in one step a bond = > > ; rotates over more degrees than = > > lincs-warnangle = 30 > > ; Periodic boundary conditions: xyz, no, xy > > pbc = xyz > > periodic_molecules = no > > ; nblist cut-off > > rlist= 1 > > > > ; OPTIONS FOR ELECTROSTATICS AND VDW > > ; Method for doing electrostatics > > coulombtype = Ewald > > rcoulomb = 1 > > ; Method for doing Van der Waals > > vdw-type = Cut-off > > ; cut-off lengths > > rvdw = 1 > > > > ; Spacing for the PME/PPPM FFT grid > > fourierspacing = 0.12 > > ; FFT grid size, when a value is 0 fourierspacing will be used > > fourier_nx = 0 > > fourier_ny = 0 > > fourier_nz = 0 > > ; EWALD/PME/PPPM parameters > > pme_order= 6 > > ewald_rtol = 1e-4 > > ewald_geometry = 3d > > epsilon_surface = 0 > > opti
[gmx-users] Compiling Gromacs 4.0.7 on AIX 5.3
This worked for me on AIX 5.3 for gromacs 4.0.4, I didn't try to compile any gromacs versions after that because we found that gromacs runs much better on Xeons and Opterons than it runs on power6's running AIX 5.3 If you have a problem specific to 4.0.7 (i.e. you can compile 4.0.4 alright on AIX 5.3), then I'm sorry but I can not help you there. Note: be sure to modify the /scratch/cneale lines to match your system. Note: the -O5 flag makes this compilation take about 20h. You should probably try without it first (~30 minute - 1h compilation), but it does giev a few extra percent speed. Chris. ##serial compilation export PATH=/usr/lpp/ppe.hpct/bin:/usr/vacpp/bin:.:/usr/bin:/etc:/usr/sbin:/usr/ucb:/usr/bin/X11:/sbin:/usr/java14/jre/bin:/usr/java14/bin:/usr/lpp/LoadL/full/bin:/usr/local/bin export F77=xlf_r export CC=xlc_r export CXX=xlc++_r export FFLAGS="-O5 -qarch=pwr6 -qtune=pwr6" export CFLAGS="-O5 -qarch=pwr6 -qtune=pwr6" export CXXFLAGS="-O5 -qarch=pwr6 -qtune=pwr6" export FFTW_LOCATION=/scratch/cneale/exe/fftw-3.1.2_aix/exec export GROMACS_LOCATION=/scratch/cneale/exe/gromacs-4.0.4_aix/exec export CPPFLAGS=-I$FFTW_LOCATION/include export LDFLAGS=-L$FFTW_LOCATION/lib cd /scratch/cneale/exe/gromacs-4.0.4_aix mkdir exec ./configure --prefix=$GROMACS_LOCATION --without-motif-includes --without-motif-libraries --without-x --without-xml >output.configure 2>&1 make >output.make 2>&1 make install >output.make_install 2>&1 make distclean # ##parallel compilation export F77=xlf_r export CC=xlc_r export CXX=xlc++_r export FFLAGS="-O5 -qarch=pwr6 -qtune=pwr6" export CFLAGS="-O5 -qarch=pwr6 -qtune=pwr6" export CXXFLAGS="-O5 -qarch=pwr6 -qtune=pwr6" export FFTW_LOCATION=/scratch/cneale/exe/fftw-3.1.2_aix/exec export GROMACS_LOCATION=/scratch/cneale/exe/gromacs-4.0.4_aix/exec export CPPFLAGS=-I$FFTW_LOCATION/include export LDFLAGS=-L$FFTW_LOCATION/lib cd /scratch/cneale/exe/gromacs-4.0.4_aix echo "cn-r0-10" > ~/.rhosts echo localhost > ~/host.list for((i=2;i<=16;i++)); do echo localhost >> ~/host.list done export MP_HOSTFILE=~/host.list ./configure --prefix=$GROMACS_LOCATION --without-motif-includes --without-motif-libraries --without-x --without-xml --enable-mpi --disable-nice --program-suffix="_mpi" CC=mpcc_r F77=mpxlf_r > output.configure_mpi 2>&1 make mdrun > output.make_mpi 2>&1 make install-mdrun > output.make_install_mpi 2>&1 make distclean -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] Compiling Gromacs 4.0.7 on AIX 5.3
Dear All, I have problems with Compiling Gromacs 4.0.7 on AIX 5.3 using gromacs 4.0.7 and fftw 3.2.2 here is what I do for FFTW : ./configure --enable-float make make install everything works fine after that, I do some variable settings : export CC='xlc_r' export F77='xlf_r' export FFLAGS='-O0 -q64' export CFLAGS='-O0 -q64' export AR='ar -X 64' export LDFLAGS='-L/usr/local/lib' export CPPFLAGS='-I/usr/local/include' then I try to compile Gromacs : ./configure (it's ok) make unfortunately it ends like that : xlc_r -O0 -q64 -o grompp grompp.o -L/usr/local/lib/ ./.libs/libgmxpreprocess.a -L/users3/olivap/sb/p64/export/power_510_32/usr/lib -L/gestconf/project/GNOME_ACL/GNOME/build/sh_dev_GNOME/export/power_510_32/usr/lib -L/gestconf/project/GNOME_ACL/GNOME/build/latest/export/power_510_32/usr/lib -L/users/project/PDP/PDP_51_050/usr/ccs/lib -L/users/project/PDP/PDP_51_050/usr/lib -L/users3/olivap/sb/p64/export/power_510_32/usr/lib/python2.2/config/ -L/usr/lpp/xlf/lib ../mdlib/.libs/libmd.a /p5cecic/home/smorin/gromacs-4.0.7/src/gmxlib/.libs/libgmx.a ../gmxlib/.libs/libgmx.a -L/opt/freeware/lib -lxml2 -ldl -lpthread -lz -liconv -lnsl /usr/local/lib/libfftw3f.a -lSM -lICE -lX11 -lxlf90 -lxlopt -lxlf -lxlomp_ser -lpthreads -lm -Wl,-blibpath:/opt/freeware/lib:/usr/local/lib/:/usr/vac/lib:/usr/lib/threads:/usr/lib:/lib ld: 0711-317 ERROR: Undefined symbol: .fftwf_destroy_plan ld: 0711-317 ERROR: Undefined symbol: .fftwf_free ld: 0711-317 ERROR: Undefined symbol: .fftwf_execute_dft_r2c ld: 0711-317 ERROR: Undefined symbol: .fftwf_execute_dft_c2r ld: 0711-317 ERROR: Undefined symbol: .fftwf_execute_dft ld: 0711-317 ERROR: Undefined symbol: .fftwf_malloc ld: 0711-317 ERROR: Undefined symbol: .fftwf_plan_dft_c2r_3d ld: 0711-317 ERROR: Undefined symbol: .fftwf_plan_dft_r2c_3d ld: 0711-317 ERROR: Undefined symbol: .fftwf_plan_dft_3d ld: 0711-317 ERROR: Undefined symbol: .fftwf_plan_dft_c2r_2d ld: 0711-317 ERROR: Undefined symbol: .fftwf_plan_dft_r2c_2d ld: 0711-317 ERROR: Undefined symbol: .fftwf_plan_dft_2d ld: 0711-317 ERROR: Undefined symbol: .fftwf_plan_dft_c2r_1d ld: 0711-317 ERROR: Undefined symbol: .fftwf_plan_dft_r2c_1d ld: 0711-317 ERROR: Undefined symbol: .fftwf_plan_dft_1d ld: 0711-345 Use the -bloadmap or -bnoquiet option to obtain more information. make: 1254-004 The error code from the last command is 8. Stop. make: 1254-004 The error code from the last command is 1. Stop. make: 1254-004 The error code from the last command is 2. Stop. make: 1254-004 The error code from the last command is 1. Stop. If anyone has an idea of need complementary informations ? Thanks a lot :-) <>-- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] CG-MD simulation of protein, always crash with protein
My target system is a protein with lipid molecules added randomly (using
GENBOX). Running MD, I expect to have the protein "inserted" through
self-assembly. However, I encountered the crash every different trials. So I
broke down the problem, that is, to run md simulation for the protein
molecule only, and in vacuum. Still no improvement. Although all the
distances in the minimized structure are visually proper, the system
exploded.
When I set RING_BONDS="bonds", the system crashed at the very first step.
With RING_BONDS="constraints", it exploded at about 5800 ps. It is strange
that RMSD differences at that time has been relatively constant. with such
RMSD, I think the system must be stable enough?!?!
I built the topology using the script seq2itp provided at Martini's site.
Already did some random check to see if the script works fine, special
notice was made at amino acids with ring. Should I make a more thorough
check on the itp file?
Trang
On Thu, Apr 15, 2010 at 6:32 PM, XAvier Periole wrote:
>
> It is mot likely that your preparation of the system is somehow corrupted.
> The insertion of a protein in a lipid bilayer might easily introduce strong
> forces in the system and thereby result in a crash of your simulation.
>
> It is also possible that your protein topology is not describing your
> system
> correctly. This no one can tell without knowing how you built your topology
> and for which kind of system.
>
> Note that cycle in the Martini FF (Tyr/Trp/His) use constrains and are
> therefore extremely sensible to strong forces in there environment.
>
> I would suggest you get back to the point where you insert your protein
> in the bilayer and check very carefully potential bad contact between the
> protein and the lipid. The minimization should go smooth and running
> should not be problematic.
>
> XAvier.
>
> On Apr 15, 2010, at 12:49 PM, Trang wrote:
>
> Dear gmx users,
> I'm trying to run some CG-MD with gromacs, using the available Martini FF.
> The first run with {lipid + water} is fine. The POPC lipid bilayer is
> successfully self-assembled. I then applied Martini FF for system involving
> protein.
> All the systems I've tried so far could not survive an md run for long
> enough. Most of them crashed at the very first step.
>
> I've encountered different types of errors (range checking error,
> segmentation fault...) and even hanging of the system, all of which converge
> at the same suggestion that the system hasn't been minimized/equilibrated
> well enough.
>
> I've tried some tracing back but still cannot figure out where the problem
> can be.
>
> * From screen output, I traced back to the atoms on which large force
> affect: most of the cases, these atoms belong to the ring of amino acid such
> as TRP, TYR. The worst case was that, 2 beads of 1 TRP totally overlap after
> minimization!!! The newest trial is related to atom 195 - 196 - 197, which
> are beads of the same TYR
> residue.
> What kind of problem can cause such a bad minimization?
>
> * From log file after crashed runs, I found the initial temperature is
> extremely high (e.g 6.67074e+12 K, etc). A colleague of mine suggest that it
> may be due to the high pressure, which in turn caused by unevenly
> distributed molecules in the input structure. This seemed to be reasonable,
> for after minimization
> (picture),
> the distribution of water is even worse than the initial state (
> picture).
> But, I get stuck and have no idea why minimization can make system so bad.
> This is the mdp for the minimization step
>
> ---MINI---
> title= Martini
> cpp = /usr/bin/cpp
> integrator = steep
> tinit= 0.0
> dt = 0.025
> nsteps = 500
> nstcomm = 1
> comm-grps=
> nstxout = 5000
> nstvout = 5000
> nstfout = 0
> nstlog = 1000
> nstenergy= 1000
> nstxtcout= 1000
> xtc_precision= 100
> xtc-grps =
> energygrps =
> nstlist = 10
> ns_type = grid
> pbc = xyz
> rlist= 1.2
> coulombtype = Shift
> rcoulomb_switch = 0.0
> rcoulomb = 1.2
> epsilon_r= 15
> vdw_type = Shift
> rvdw_switch = 0.9
> rvdw = 1.2
> DispCorr = No
> tcoupl = no
> Pcoupl = no
> gen_vel = no
> gen_temp = 320
> gen_seed = 473529
[gmx-users] Concerns with g_wham
I have been using g_wham, but I have a few questions that I can't find answers to online. When using WHAM, one does not need the forces between the pull groups to calculate the PMF, yet g_wham won't run without it. Is there a reason for this? I have never used g_wham, but g_wham -h (gromacs-4.0.5) indicates that you are incorrect (see below). The short answer is probably to use g_wham -h to see that -ix and -if are optional and read the information at the top to see that you should not use both at once. If you still have problems, please be more explicit like this: "With gromacs version X, I did A (copy text of command here) and I got error message B (copy error message here), and the output file looked like C (copy output file snippit here)... But when I do A2 I get B2, etc." here is a snippit from g_wham -h : At present, three input modes are supported. * With option -it, the user provides a file which contains the filenames of the umbrella simulation run-input files (tpr files), AND, with option -ix, a file which contains filenames of the pullx mdrun output files. The tpr and pullx files must be in corresponding order, i.e. the first tpr created the first pullx, etc. * Same as the previous input mode, except that the the user provides the pull force ouput file names (pullf.xvg) with option -if. From the pull force the position in the ubrella potential is computed. This does not work with tabulated umbrella potentials. * With option -ip, the user provides filenames of (gzipped) pdo files, i.e. the gromacs 3.3 umbrella output files. If you have some unusual reaction coordinate you may also generate your own pdo files and feed them with the -ip option into to g_wham. The pdo file header must be similar to the folowing: Also, when using the pull code, I am allowed to define the spring constant K for umbrella sampling, but I do not designate where the umbrella potential is centered. How does gromacs determine this? I am interested as I would like to create a PMF using umbrella integration (from code I will write myself) rather than use WHAM. To do this and still use the umbrella sampling runs used with GROMACS, I need to know where my umbrella potentials are centered. This is outlined in the online .mdp options section of the manual (again for gromacs 4): http://manual.gromacs.org/current/online/mdp_opt.html#pull I think everybody agrees that the manual would benefit from some more description about how the pull code works, especially in version 4, but the information that is there should at least get farther than you are now... It's one of those things where the information is all there but this is only obvious once you already understand how it works ;) Chris. -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] slow speed
Hello, On 15.04.2010, at 16:18, Mark Abraham wrote: > On 16/04/2010 12:02 AM, Shuangxing Dai wrote: >> Hi, gmx-users: >>I am using latest version of gromacs and found it was really slow. I >> was wondering anyone got the same experience and can point out where the >> problem is. >>I was running double precision for MD. But for each dynamics >> simulation, it takes 4 days. I should only take two or three hours. > > Well, double precisions is slower - possibly very much so. You need twice the > bus and cache bandwidth because you are throwing around twice the memory. > Otherwise, we can't say much because we don't know anything about your > hardware or where you got your benchmark from. > > Other comments below. It looks very much like you've gone and made a bunch of > semi-random changes to things. That's not normally a good idea. > >>Here is the .mdp file: >> define = >> ; RUN CONTROL PARAMETERS = >> integrator = sd >> ; start time and timestep in ps = >> tinit= 0 >> dt = 0.001 >> nsteps = 20 >> ; number of steps for center of mass motion removal = >> nstcomm = 100 >> ; OUTPUT CONTROL OPTIONS = >> ; Output frequency for coords (x), velocities (v) and forces (f) = >> nstxout = 0 >> nstvout = 0 >> nstfout = 0 >> ; Output frequency for energies to log file and energy file = >> nstlog = 100 >> nstenergy= 100 >> ; Output frequency and precision for xtc file = >> nstxtcout= 100 >> xtc-precision= 1000 >> ; NEIGHBORSEARCHING PARAMETERS = >> ; nblist update frequency = >> nstlist = 50 >> ; ns algorithm (simple or grid) = >> ns_type = grid >> >> ;OPTIONS FOR PRESSURE COUPLING >> Pcoupl = berendsen >> tau_p= 1 >> compressibility = 4.5e-05 >> ref_p= 0.1 >> ;OPTIONS FOR TEMPERATURE COUPLING >> tc_grps = system >> tau_t= 0.1 >> ref_t= 300 >> ; OPTIONS FOR BONDS = >> constraints = hbonds >> ; Type of constraint algorithm = >> constraint-algorithm = Lincs >> ; Do not constrain the start configuration = >> unconstrained-start = no >> ; Relative tolerance of shake = >> shake-tol= 0.0001 >> ; Highest order in the expansion of the constraint coupling matrix = >> lincs-order = 12 > > That's huge, and the use of lincs is somewhat inconsistent with a 1fs > timestep. > >> ; Lincs will write a warning to the stderr if in one step a bond = >> ; rotates over more degrees than = >> lincs-warnangle = 30 >> ; Periodic boundary conditions: xyz, no, xy >> pbc = xyz >> periodic_molecules = no >> ; nblist cut-off >> rlist= 1 >> >> ; OPTIONS FOR ELECTROSTATICS AND VDW >> ; Method for doing electrostatics >> coulombtype = Ewald > > This could be a correct decision, but it's unlikely. > >> rcoulomb = 1 >> ; Method for doing Van der Waals >> vdw-type = Cut-off >> ; cut-off lengths >> rvdw = 1 >> >> ; Spacing for the PME/PPPM FFT grid >> fourierspacing = 0.12 >> ; FFT grid size, when a value is 0 fourierspacing will be used >> fourier_nx = 0 >> fourier_ny = 0 >> fourier_nz = 0 >> ; EWALD/PME/PPPM parameters >> pme_order= 6 >> ewald_rtol = 1e-4 > > Again, could be correct, or could just be killing you. > This is definitely killing you, because you can run Ewald just in serial and not in parallel. Cheers, Flo >> ewald_geometry = 3d >> epsilon_surface = 0 >> optimize_fft = no > > Mark > -- > gmx-users mailing listgmx-users@gromacs.org > http://lists.gromacs.org/mailman/listinfo/gmx-users > Please search the archive at http://www.gromacs.org/search before posting! > Please don't post (un)subscribe requests to the list. Use the www interface > or send it to gmx-users-requ...@gromacs.org. > Can't post? Read http://www.gromacs.org/mailing_lists/users.php -- Florian Dommert Dipl.-Phys. Institute for Computational Physics University Stuttgart Pfaffenwaldring 27 70569 Stuttgart Phone: +49(0)711/685-6-3613 Fax: +49-(0)711/685-6-3658 EMail: domm...@icp.uni-stuttgart.de Home: http://www.icp.uni-stuttgart.de/~icp/Florian_Dommert PGP.sig Description: This is a digitally signed message part -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.
Re: [gmx-users] slow speed
On 16/04/2010 12:02 AM, Shuangxing Dai wrote: Hi, gmx-users: I am using latest version of gromacs and found it was really slow. I was wondering anyone got the same experience and can point out where the problem is. I was running double precision for MD. But for each dynamics simulation, it takes 4 days. I should only take two or three hours. Well, double precisions is slower - possibly very much so. You need twice the bus and cache bandwidth because you are throwing around twice the memory. Otherwise, we can't say much because we don't know anything about your hardware or where you got your benchmark from. Other comments below. It looks very much like you've gone and made a bunch of semi-random changes to things. That's not normally a good idea. Here is the .mdp file: define = ; RUN CONTROL PARAMETERS = integrator = sd ; start time and timestep in ps = tinit= 0 dt = 0.001 nsteps = 20 ; number of steps for center of mass motion removal = nstcomm = 100 ; OUTPUT CONTROL OPTIONS = ; Output frequency for coords (x), velocities (v) and forces (f) = nstxout = 0 nstvout = 0 nstfout = 0 ; Output frequency for energies to log file and energy file = nstlog = 100 nstenergy= 100 ; Output frequency and precision for xtc file = nstxtcout= 100 xtc-precision= 1000 ; NEIGHBORSEARCHING PARAMETERS = ; nblist update frequency = nstlist = 50 ; ns algorithm (simple or grid) = ns_type = grid ;OPTIONS FOR PRESSURE COUPLING Pcoupl = berendsen tau_p= 1 compressibility = 4.5e-05 ref_p= 0.1 ;OPTIONS FOR TEMPERATURE COUPLING tc_grps = system tau_t= 0.1 ref_t= 300 ; OPTIONS FOR BONDS = constraints = hbonds ; Type of constraint algorithm = constraint-algorithm = Lincs ; Do not constrain the start configuration = unconstrained-start = no ; Relative tolerance of shake = shake-tol= 0.0001 ; Highest order in the expansion of the constraint coupling matrix = lincs-order = 12 That's huge, and the use of lincs is somewhat inconsistent with a 1fs timestep. ; Lincs will write a warning to the stderr if in one step a bond = ; rotates over more degrees than = lincs-warnangle = 30 ; Periodic boundary conditions: xyz, no, xy pbc = xyz periodic_molecules = no ; nblist cut-off rlist= 1 ; OPTIONS FOR ELECTROSTATICS AND VDW ; Method for doing electrostatics coulombtype = Ewald This could be a correct decision, but it's unlikely. rcoulomb = 1 ; Method for doing Van der Waals vdw-type = Cut-off ; cut-off lengths rvdw = 1 ; Spacing for the PME/PPPM FFT grid fourierspacing = 0.12 ; FFT grid size, when a value is 0 fourierspacing will be used fourier_nx = 0 fourier_ny = 0 fourier_nz = 0 ; EWALD/PME/PPPM parameters pme_order= 6 ewald_rtol = 1e-4 Again, could be correct, or could just be killing you. ewald_geometry = 3d epsilon_surface = 0 optimize_fft = no Mark -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] slow speed
What makes you think it should be so fast? Nothing appears obviously wrong in the mdp file. May be this though! lincs-order = 12 On Apr 15, 2010, at 4:02 PM, Shuangxing Dai wrote: Hi, gmx-users: I am using latest version of gromacs and found it was really slow. I was wondering anyone got the same experience and can point out where the problem is. I was running double precision for MD. But for each dynamics simulation, it takes 4 days. I should only take two or three hours. Here is the .mdp file: define = ; RUN CONTROL PARAMETERS = integrator = sd ; start time and timestep in ps = tinit= 0 dt = 0.001 nsteps = 20 ; number of steps for center of mass motion removal = nstcomm = 100 ; OUTPUT CONTROL OPTIONS = ; Output frequency for coords (x), velocities (v) and forces (f) = nstxout = 0 nstvout = 0 nstfout = 0 ; Output frequency for energies to log file and energy file = nstlog = 100 nstenergy= 100 ; Output frequency and precision for xtc file = nstxtcout= 100 xtc-precision= 1000 ; NEIGHBORSEARCHING PARAMETERS = ; nblist update frequency = nstlist = 50 ; ns algorithm (simple or grid) = ns_type = grid ;OPTIONS FOR PRESSURE COUPLING Pcoupl = berendsen tau_p= 1 compressibility = 4.5e-05 ref_p= 0.1 ;OPTIONS FOR TEMPERATURE COUPLING tc_grps = system tau_t= 0.1 ref_t= 300 ; OPTIONS FOR BONDS = constraints = hbonds ; Type of constraint algorithm = constraint-algorithm = Lincs ; Do not constrain the start configuration = unconstrained-start = no ; Relative tolerance of shake = shake-tol= 0.0001 ; Highest order in the expansion of the constraint coupling matrix = lincs-order = 12 ; Lincs will write a warning to the stderr if in one step a bond = ; rotates over more degrees than = lincs-warnangle = 30 ; Periodic boundary conditions: xyz, no, xy pbc = xyz periodic_molecules = no ; nblist cut-off rlist= 1 ; OPTIONS FOR ELECTROSTATICS AND VDW ; Method for doing electrostatics coulombtype = Ewald rcoulomb = 1 ; Method for doing Van der Waals vdw-type = Cut-off ; cut-off lengths rvdw = 1 ; Spacing for the PME/PPPM FFT grid fourierspacing = 0.12 ; FFT grid size, when a value is 0 fourierspacing will be used fourier_nx = 0 fourier_ny = 0 fourier_nz = 0 ; EWALD/PME/PPPM parameters pme_order= 6 ewald_rtol = 1e-4 ewald_geometry = 3d epsilon_surface = 0 optimize_fft = no Can anyone help me? Thank you in advance. Thanks, Shuangxing Dai -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] slow speed
Shuangxing Dai wrote: Hi, gmx-users: I am using latest version of gromacs and found it was really slow. I was wondering anyone got the same experience and can point out where the problem is. I was running double precision for MD. But for each dynamics simulation, it takes 4 days. I should only take two or three hours. How did you establish this benchmark? Are you running in serial or in parallel? If you're running in parallel, what type of interconnect do the processors have? If they're high-latency (like gigabit ethernet) you will not get very good performance. -Justin Here is the .mdp file: define = ; RUN CONTROL PARAMETERS = integrator = sd ; start time and timestep in ps = tinit= 0 dt = 0.001 nsteps = 20 ; number of steps for center of mass motion removal = nstcomm = 100 ; OUTPUT CONTROL OPTIONS = ; Output frequency for coords (x), velocities (v) and forces (f) = nstxout = 0 nstvout = 0 nstfout = 0 ; Output frequency for energies to log file and energy file = nstlog = 100 nstenergy= 100 ; Output frequency and precision for xtc file = nstxtcout= 100 xtc-precision= 1000 ; NEIGHBORSEARCHING PARAMETERS = ; nblist update frequency = nstlist = 50 ; ns algorithm (simple or grid) = ns_type = grid ;OPTIONS FOR PRESSURE COUPLING Pcoupl = berendsen tau_p= 1 compressibility = 4.5e-05 ref_p= 0.1 ;OPTIONS FOR TEMPERATURE COUPLING tc_grps = system tau_t= 0.1 ref_t= 300 ; OPTIONS FOR BONDS = constraints = hbonds ; Type of constraint algorithm = constraint-algorithm = Lincs ; Do not constrain the start configuration = unconstrained-start = no ; Relative tolerance of shake = shake-tol= 0.0001 ; Highest order in the expansion of the constraint coupling matrix = lincs-order = 12 ; Lincs will write a warning to the stderr if in one step a bond = ; rotates over more degrees than = lincs-warnangle = 30 ; Periodic boundary conditions: xyz, no, xy pbc = xyz periodic_molecules = no ; nblist cut-off rlist= 1 ; OPTIONS FOR ELECTROSTATICS AND VDW ; Method for doing electrostatics coulombtype = Ewald rcoulomb = 1 ; Method for doing Van der Waals vdw-type = Cut-off ; cut-off lengths rvdw = 1 ; Spacing for the PME/PPPM FFT grid fourierspacing = 0.12 ; FFT grid size, when a value is 0 fourierspacing will be used fourier_nx = 0 fourier_ny = 0 fourier_nz = 0 ; EWALD/PME/PPPM parameters pme_order= 6 ewald_rtol = 1e-4 ewald_geometry = 3d epsilon_surface = 0 optimize_fft = no Can anyone help me? Thank you in advance. Thanks, Shuangxing Dai -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES-IGERT Trainee Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] slow speed
Hi, gmx-users: I am using latest version of gromacs and found it was really slow. I was wondering anyone got the same experience and can point out where the problem is. I was running double precision for MD. But for each dynamics simulation, it takes 4 days. I should only take two or three hours. Here is the .mdp file: define = ; RUN CONTROL PARAMETERS = integrator = sd ; start time and timestep in ps = tinit= 0 dt = 0.001 nsteps = 20 ; number of steps for center of mass motion removal = nstcomm = 100 ; OUTPUT CONTROL OPTIONS = ; Output frequency for coords (x), velocities (v) and forces (f) = nstxout = 0 nstvout = 0 nstfout = 0 ; Output frequency for energies to log file and energy file = nstlog = 100 nstenergy= 100 ; Output frequency and precision for xtc file = nstxtcout= 100 xtc-precision= 1000 ; NEIGHBORSEARCHING PARAMETERS = ; nblist update frequency = nstlist = 50 ; ns algorithm (simple or grid) = ns_type = grid ;OPTIONS FOR PRESSURE COUPLING Pcoupl = berendsen tau_p= 1 compressibility = 4.5e-05 ref_p= 0.1 ;OPTIONS FOR TEMPERATURE COUPLING tc_grps = system tau_t= 0.1 ref_t= 300 ; OPTIONS FOR BONDS = constraints = hbonds ; Type of constraint algorithm = constraint-algorithm = Lincs ; Do not constrain the start configuration = unconstrained-start = no ; Relative tolerance of shake = shake-tol= 0.0001 ; Highest order in the expansion of the constraint coupling matrix = lincs-order = 12 ; Lincs will write a warning to the stderr if in one step a bond = ; rotates over more degrees than = lincs-warnangle = 30 ; Periodic boundary conditions: xyz, no, xy pbc = xyz periodic_molecules = no ; nblist cut-off rlist= 1 ; OPTIONS FOR ELECTROSTATICS AND VDW ; Method for doing electrostatics coulombtype = Ewald rcoulomb = 1 ; Method for doing Van der Waals vdw-type = Cut-off ; cut-off lengths rvdw = 1 ; Spacing for the PME/PPPM FFT grid fourierspacing = 0.12 ; FFT grid size, when a value is 0 fourierspacing will be used fourier_nx = 0 fourier_ny = 0 fourier_nz = 0 ; EWALD/PME/PPPM parameters pme_order= 6 ewald_rtol = 1e-4 ewald_geometry = 3d epsilon_surface = 0 optimize_fft = no Can anyone help me? Thank you in advance. Thanks, Shuangxing Dai -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] SMD simulations stops without error
Hi I pulled an ion to move along the axial direction in a nanotube by using SMD simulation, with the version of Gromacs-4.0.7. For some cases, the simulations stopped without any errors. The simulation could properly run, but it did not run to the end. The following is the pulling code in my .mdp file. ; COM PULLING ; Pull type: no, umbrella, constraint or constant_force pull = constraint ; Pull geometry: distance, direction, cylinder or position pull_geometry= direction ; Select components for the pull vector. default: Y Y Y pull_dim = N N Y ; Cylinder radius for dynamic reaction force groups (nm) pull_r1 = 1 ; Switch from r1 to r0 in case of dynamic reaction force pull_r0 = 1.5 pull_constr_tol = 1e-06 pull_start = no pull_nstxout = 10 pull_nstfout = 10 ; Number of pull groups pull_ngroups = 1 ; Group name, weight (default all 1), vector, init, rate (nm/ps), kJ/(mol*nm^2) pull_group0 = pull_weights0= pull_pbcatom0= 0 pull_group1 = Na pull_weights1= pull_pbcatom1= 0 pull_vec1= 0.0 0.0 1.0 pull_init1 = 10.500 pull_rate1 = 0.0563104 pull_k1 = pull_kB1 = Is there any parameters in the pulling code setted with improper values? Anys suggestions or answers are appreciated.-- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] CG-MD simulation of protein, always crash with protein
It is mot likely that your preparation of the system is somehow
corrupted.
The insertion of a protein in a lipid bilayer might easily introduce
strong
forces in the system and thereby result in a crash of your simulation.
It is also possible that your protein topology is not describing your
system
correctly. This no one can tell without knowing how you built your
topology
and for which kind of system.
Note that cycle in the Martini FF (Tyr/Trp/His) use constrains and are
therefore extremely sensible to strong forces in there environment.
I would suggest you get back to the point where you insert your protein
in the bilayer and check very carefully potential bad contact between
the
protein and the lipid. The minimization should go smooth and running
should not be problematic.
XAvier.
On Apr 15, 2010, at 12:49 PM, Trang wrote:
Dear gmx users,
I'm trying to run some CG-MD with gromacs, using the available
Martini FF.
The first run with {lipid + water} is fine. The POPC lipid bilayer
is successfully self-assembled. I then applied Martini FF for system
involving protein.
All the systems I've tried so far could not survive an md run for
long enough. Most of them crashed at the very first step.
I've encountered different types of errors (range checking error,
segmentation fault...) and even hanging of the system, all of which
converge at the same suggestion that the system hasn't been
minimized/equilibrated well enough.
I've tried some tracing back but still cannot figure out where the
problem can be.
* From screen output, I traced back to the atoms on which large
force affect: most of the cases, these atoms belong to the ring of
amino acid such as TRP, TYR. The worst case was that, 2 beads of 1
TRP totally overlap after minimization!!! The newest trial is
related to atom 195 - 196 - 197, which are beads of the same TYR
residue . What kind of problem can cause such a bad minimization?
* From log file after crashed runs, I found the initial temperature
is extremely high (e.g 6.67074e+12 K, etc). A colleague of mine
suggest that it may be due to the high pressure, which in turn
caused by unevenly distributed molecules in the input structure.
This seemed to be reasonable, for after minimization (picture ), the
distribution of water is even worse than the initial state
(picture). But, I get stuck and have no idea why minimization can
make system so bad. This is the mdp for the minimization step
---
MINI---
title= Martini
cpp = /usr/bin/cpp
integrator = steep
tinit= 0.0
dt = 0.025
nsteps = 500
nstcomm = 1
comm-grps=
nstxout = 5000
nstvout = 5000
nstfout = 0
nstlog = 1000
nstenergy= 1000
nstxtcout= 1000
xtc_precision= 100
xtc-grps =
energygrps =
nstlist = 10
ns_type = grid
pbc = xyz
rlist= 1.2
coulombtype = Shift
rcoulomb_switch = 0.0
rcoulomb = 1.2
epsilon_r= 15
vdw_type = Shift
rvdw_switch = 0.9
rvdw = 1.2
DispCorr = No
tcoupl = no
Pcoupl = no
gen_vel = no
gen_temp = 320
gen_seed = 473529
constraints = none
constraint_algorithm = Lincs
unconstrained_start = no
lincs_order = 4
lincs_warnangle = 30
and this is for the next step md
MD--
title= Martini
cpp = /usr/bin/cpp
integrator = md
tinit= 0.0
dt = 0.025
nsteps = 5
nstcomm = 1
comm-grps=
nstxout = 5000
nstvout = 5000
nstfout = 0
nstlog = 2000
nstenergy= 2000
nstxtcout= 1000
xtc_precision= 100
xtc-grps =
energygrps =
nstlist = 10
ns_type = grid
pbc = xyz
rlist= 1.2
coulombtype = Shift
rcoulomb_switch = 0.0
rcoulomb = 1.2
epsilon_r= 15
vdw_type = Shift
rvdw_switch = 0.9
rvdw = 1.2
DispCorr = No
tcoupl = Berendsen
tc-grps = Protein W
tau_t= 0.3 0.3
r
[gmx-users] g_sas command with the -q option
Hi all, I have a system which is composed of hexane-peptide-water-peptide-hexane layers. There, I selected the hexane+peptide system as the calculation group, and the hexane group as the output group to calculate the hexane area that is in contact with water. To do this I used the g_sas command with the -q option. I looked at the connelly.pdb file via vmd. I think the calculation and the output groups are shown in that file. I saw that the the upper, right and left sides of the simulation box have been included which means to me the periodic boundaries are not taken into account during the calculation. In addition, when I use the g_sas command I get a warning as the following: WARNING: Analysis based on vacuum simulations (with the possibility of evaporation)will certainly crash the analysis. Turning off pbc. So, the periodic boundary is taken into account or not during the sas calculation? Regards -- Ozge Engin ★☆ -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] CG-MD simulation of protein, always crash with protein
Dear gmx users,
I'm trying to run some CG-MD with gromacs, using the available Martini FF.
The first run with {lipid + water} is fine. The POPC lipid bilayer is
successfully self-assembled. I then applied Martini FF for system involving
protein.
All the systems I've tried so far could not survive an md run for long
enough. Most of them crashed at the very first step.
I've encountered different types of errors (range checking error,
segmentation fault...) and even hanging of the system, all of which converge
at the same suggestion that the system hasn't been minimized/equilibrated
well enough.
I've tried some tracing back but still cannot figure out where the problem
can be.
* From screen output, I traced back to the atoms on which large force
affect: most of the cases, these atoms belong to the ring of amino acid such
as TRP, TYR. The worst case was that, 2 beads of 1 TRP totally overlap after
minimization!!! The newest trial is related to atom 195 - 196 - 197, which
are beads of the same TYR
residue.
What kind of problem can cause such a bad minimization?
* From log file after crashed runs, I found the initial temperature is
extremely high (e.g 6.67074e+12 K, etc). A colleague of mine suggest that it
may be due to the high pressure, which in turn caused by unevenly
distributed molecules in the input structure. This seemed to be reasonable,
for after minimization
(picture),
the distribution of water is even worse than the initial state (
picture).
But, I get stuck and have no idea why minimization can make system so bad.
This is the mdp for the minimization step
---MINI---
title= Martini
cpp = /usr/bin/cpp
integrator = steep
tinit= 0.0
dt = 0.025
nsteps = 500
nstcomm = 1
comm-grps=
nstxout = 5000
nstvout = 5000
nstfout = 0
nstlog = 1000
nstenergy= 1000
nstxtcout= 1000
xtc_precision= 100
xtc-grps =
energygrps =
nstlist = 10
ns_type = grid
pbc = xyz
rlist= 1.2
coulombtype = Shift
rcoulomb_switch = 0.0
rcoulomb = 1.2
epsilon_r= 15
vdw_type = Shift
rvdw_switch = 0.9
rvdw = 1.2
DispCorr = No
tcoupl = no
Pcoupl = no
gen_vel = no
gen_temp = 320
gen_seed = 473529
constraints = none
constraint_algorithm = Lincs
unconstrained_start = no
lincs_order = 4
lincs_warnangle = 30
and this is for the next step md
MD--
title= Martini
cpp = /usr/bin/cpp
integrator = md
tinit= 0.0
dt = 0.025
nsteps = 5
nstcomm = 1
comm-grps=
nstxout = 5000
nstvout = 5000
nstfout = 0
nstlog = 2000
nstenergy= 2000
nstxtcout= 1000
xtc_precision= 100
xtc-grps =
energygrps =
nstlist = 10
ns_type = grid
pbc = xyz
rlist= 1.2
coulombtype = Shift
rcoulomb_switch = 0.0
rcoulomb = 1.2
epsilon_r= 15
vdw_type = Shift
rvdw_switch = 0.9
rvdw = 1.2
DispCorr = No
tcoupl = Berendsen
tc-grps = Protein W
tau_t= 0.3 0.3
ref_t= 323 323
Pcoupl = berendsen
Pcoupltype = isotropic
tau_p= 3.0
compressibility = 3e-5
ref_p= 1.0
gen_vel = no
gen_temp = 323
gen_seed = 666
constraints = none
constraint_algorithm = Lincs
unconstrained_start = no
lincs_order = 4
lincs_warnangle = 30
I've struggled with this for about 2 weeks and still have no idea of where
to fix the problem. Am I missing something too basic for tutorials to
Re: [gmx-users] Re: ffcharmm27 for HEME
Hi Par and Mark, Thanks for the suggestions. You may be correct, using gromacs version 4.0.5 Charmm ff didn't worked straight away in my first attempt, but it works after i made some modification here and there. Best regards, Rama On Thu, Apr 15, 2010 at 2:47 AM, Pär Bjelkmar wrote: > Hi, > > 15 apr 2010 kl. 11.11 skrev Ramachandran G: > > Hello Par: >Using the latest git i could able to work on my oxy-hemoglobin > system with new gromacs version 4.0.5 successfully. > > CHARMM is not supportd in version 4.0.5, you probably mean the developer > version? > > But since my new gromacs version was not installed in parallel i tried > using older version of gromacs 3.3.1 which was installed in parrallel. While > doing grompp to get the *.tpr file, i am getting the below error. > > - > Program grompp, VERSION 3.3.1 > Source code file: topdirs.c, line: 103 > > Fatal error: > Invalid dihedral type 9 > > -- > > This is because we have made changes in the source code to allow for the > CHARMM ff (we added a new dihedral type, see paper, that is causing this > particular error). So, you have to run with the developer git version. > > Regards, > Pär > > > I am planning to install the newer gromacs version also in parallel but in > the mean time i also wanted to rectify the above error, if i can. Thank > you. > > Rama > > > On Thu, Mar 18, 2010 at 3:02 AM, Pär Bjelkmar wrote: > >> Hi, >> >> I have now added the charmm files to git head and the protein and lipid >> parts should work at least. Simply check out the latest git and the charmm >> parameters should show up in pdb2gmx. >> >> /Pär >> >> 11 mar 2010 kl. 03.04 skrev Ramachandran G: >> >> Hello Bjelkumar, >> Thanks for your reply. I will wait until you add the new force >> field to the git. >> >> regards, >> rama >> >> On Tue, Mar 2, 2010 at 12:47 AM, Pär Bjelkmar wrote: >> >>> Hello, >>> >>> I have that on my schedule for next week. That is to add the new force >>> field format to the git source code tree. Until then you could use the old >>> format if you checkout a previous version of the source code. I guess you >>> know about git otherwise there's some info here >>> http://www.gromacs.org/Developer_Zone/Git/Basic_Git_Usage >>> >>> So start by getting a copy of the latest _developing_ version (git head) >>> of gromacs source code: >>> $ git clone g...@git.gromacs.org:gromacs.git >>> The force field files were update in end of January to you could checkout >>> a version from Jan 27 by: >>> $ git checkout d80138d720fd41a5005238adecd5bfd5400e524c >>> >>> then compile. Now it should work if you got the HEME parameters from >>> Michel. Alternatively you wait until end of next week when I think I have >>> had time to add the new force field format to the git head. >>> >>> Good luck! >>> /Pär >>> >>> 1 mar 2010 kl. 21.21 skrev Ramachandran G: >>> >>> Dear Pär Bjelkmar, >>> After getting help from Michel Cuendet still i am facing problem >>> and i >>> understood that in groamcs latest version 4.0.x problems may come due to >>> CMAP. >>> He suggested me to seek your help. Could you help me to get new toplogy >>> format charmm files which can adapt the HEME sections to that. >>> Thank you. >>> >>> Rama >>> >>> -- Forwarded message -- >>> From: Michel Cuendet >>> Date: Fri, Feb 26, 2010 at 1:03 PM >>> Subject: Re: ffcharmm27 for HEME >>> To: Ramachandran G >>> >>> >>> >>> Dear Mr. Ramachandran, >>> >>> This means you are using grompp from the distribution version 4.0.x. >>> This version of gromacs does not know about the CMAP forcefield term. >>> You have two options : >>> >>> 1) Deactivate CMAP. This would be equivalent to using the charmm22 ff >>> instead of the charmm27, which many people consider fine. To do this, >>> edit the file ffcharmm27.rtp and delete all [cmap] sections. This >>> _should_ work. >>> >>> 2) Download the git development version, which knows how to handle CMAP. >>> I know they have been changing topology formats in the latest versions, >>> but I hope it is still able to read the old topologies. Otherwise, you >>> will have to ask Par Bjelkmar for the charmm files in the new topology >>> format, and adapt the HEME sections to that. >>> >>> Sorry it is a bit messy at the moment. But everything should become part >>> of the gormacs4.1 distribution. >>> >>> Bye, >>> Michel >>> >>> Ramachandran G wrote: >>> > Dear Mr. Michel, >>> > Thank you very much for you help and time. >>> > Although i could able to do pdb2gmx and get the *.top file still, i >>> > have problem in getting the 'tpr' file using grompp. This is due the >>> > 'cmap' >>> > >>> > I would try to fix the problem myself but still if the problem persist >>> > then i will get back to you. Thank you again. >>> > >>> > regards, >>> > Rama >>> >
[gmx-users] Re: ffcharmm27 for HEME
Hi, 15 apr 2010 kl. 11.11 skrev Ramachandran G: > Hello Par: >Using the latest git i could able to work on my oxy-hemoglobin system > with new gromacs version 4.0.5 successfully. CHARMM is not supportd in version 4.0.5, you probably mean the developer version? > But since my new gromacs version was not installed in parallel i tried using > older version of gromacs 3.3.1 which was installed in parrallel. While doing > grompp to get the *.tpr file, i am getting the below error. > - > Program grompp, VERSION 3.3.1 > Source code file: topdirs.c, line: 103 > > Fatal error: > Invalid dihedral type 9 > -- This is because we have made changes in the source code to allow for the CHARMM ff (we added a new dihedral type, see paper, that is causing this particular error). So, you have to run with the developer git version. Regards, Pär > > I am planning to install the newer gromacs version also in parallel but in > the mean time i also wanted to rectify the above error, if i can. Thank you. > > Rama > > > On Thu, Mar 18, 2010 at 3:02 AM, Pär Bjelkmar wrote: > Hi, > > I have now added the charmm files to git head and the protein and lipid parts > should work at least. Simply check out the latest git and the charmm > parameters should show up in pdb2gmx. > > /Pär > > 11 mar 2010 kl. 03.04 skrev Ramachandran G: > >> Hello Bjelkumar, >> Thanks for your reply. I will wait until you add the new force >> field to the git. >> >> regards, >> rama >> >> On Tue, Mar 2, 2010 at 12:47 AM, Pär Bjelkmar wrote: >> Hello, >> >> I have that on my schedule for next week. That is to add the new force field >> format to the git source code tree. Until then you could use the old format >> if you checkout a previous version of the source code. I guess you know >> about git otherwise there's some info here >> http://www.gromacs.org/Developer_Zone/Git/Basic_Git_Usage >> >> So start by getting a copy of the latest _developing_ version (git head) of >> gromacs source code: >> $ git clone g...@git.gromacs.org:gromacs.git >> The force field files were update in end of January to you could checkout a >> version from Jan 27 by: >> $ git checkout d80138d720fd41a5005238adecd5bfd5400e524c >> >> then compile. Now it should work if you got the HEME parameters from Michel. >> Alternatively you wait until end of next week when I think I have had time >> to add the new force field format to the git head. >> >> Good luck! >> /Pär >> >> 1 mar 2010 kl. 21.21 skrev Ramachandran G: >> >>> Dear Pär Bjelkmar, >>> After getting help from Michel Cuendet still i am facing problem >>> and i >>> understood that in groamcs latest version 4.0.x problems may come due to >>> CMAP. >>> He suggested me to seek your help. Could you help me to get new toplogy >>> format charmm files which can adapt the HEME sections to that. >>> Thank you. >>> >>> Rama >>> >>> -- Forwarded message -- >>> From: Michel Cuendet >>> Date: Fri, Feb 26, 2010 at 1:03 PM >>> Subject: Re: ffcharmm27 for HEME >>> To: Ramachandran G >>> >>> >>> >>> Dear Mr. Ramachandran, >>> >>> This means you are using grompp from the distribution version 4.0.x. >>> This version of gromacs does not know about the CMAP forcefield term. >>> You have two options : >>> >>> 1) Deactivate CMAP. This would be equivalent to using the charmm22 ff >>> instead of the charmm27, which many people consider fine. To do this, >>> edit the file ffcharmm27.rtp and delete all [cmap] sections. This >>> _should_ work. >>> >>> 2) Download the git development version, which knows how to handle CMAP. >>> I know they have been changing topology formats in the latest versions, >>> but I hope it is still able to read the old topologies. Otherwise, you >>> will have to ask Par Bjelkmar for the charmm files in the new topology >>> format, and adapt the HEME sections to that. >>> >>> Sorry it is a bit messy at the moment. But everything should become part >>> of the gormacs4.1 distribution. >>> >>> Bye, >>> Michel >>> >>> Ramachandran G wrote: >>> > Dear Mr. Michel, >>> > Thank you very much for you help and time. >>> > Although i could able to do pdb2gmx and get the *.top file still, i >>> > have problem in getting the 'tpr' file using grompp. This is due the >>> > 'cmap' >>> > >>> > I would try to fix the problem myself but still if the problem persist >>> > then i will get back to you. Thank you again. >>> > >>> > regards, >>> > Rama >>> > >>> > On Thu, Feb 25, 2010 at 8:59 AM, Michel Cuendet >>> > mailto:michel.cuen...@isb-sib.ch>> wrote: >>> > >>> > >>> > Dear Mr. Ramachandran, >>> > >>> > Attached is a tar file containing the ffcharmm27 forcefield files >>> > modified for the HEME and an optional CO ligand. >>> > >>> > Note that
Re: [gmx-users] Time for equilibration
for the position restrain simulations have a llok at : http://www.gromacs.org/Documentation/How-tos/Position_Restraints Starting from an homology model you should expect some relaxation of the structure during the simulation. On Apr 15, 2010, at 11:06 AM, sonali dhindwal wrote: Thanks for the answer, My protein strucutre is a homology model,,on which i want to do the simulation. and the change in conformation after MD simulation is more than RMSD of 2 Angstrom, that too in the active site of the protein and you said that "Using position restrain on the heavy atoms of the protein first, and then on the Calphas is generally a good idea." How we can do this ?? and you also mentioned that time period could b increased from 100 to 500 ps, does increase in time will be helpful in not distorting the strucutre ? Regards -- Sonali Dhindwal --- On Thu, 15/4/10, XAvier Periole wrote: From: XAvier Periole Subject: Re: [gmx-users] Time for equilibration To: "Discussion list for GROMACS users" Date: Thursday, 15 April, 2010, 1:46 PM The distortion of a protein starting structure can result from various reasons: 1- experimental determination of the structure: this include the experimental conditions (T, pH) as well as the crystal contacts if X-ray were used, dynamics of some part of the molecule if NMR. 2- the manner you solvate and equilibrate. Using position restrain on the heavy atoms of the protein first, and then on the Calphas is generally a good idea. The time you need to run those simulations depends on the system. If you see deviations you can try to run a bit longer. 100 ps is generally sufficient but can be extended to 500 ps, this is no problem. 3- the force field you are using might also trigger some "small" deviations of the protein. The protein structure might contain "strange" local configuration that are not sable in the FF. 4- you set up, meaning time step, temperature, pressure, ... Note finally that a deviation from the starting structure might just be a fluctuation of a labile region of the protein ... On Apr 15, 2010, at 8:40 AM, sonali dhindwal wrote: Hello All, I have a protein of 576 amino acid long, and has a barell shape topolgy. I have done MD simulation on it for 1ns, and my protein has got distorted shape, i.e, one of the strand became coil and other strands became small. I wrote this query before also, can it be possible that this is due to equilibration conditons i am giving, i am equilibrating it for 100 ps under NVT using brendenson coupling. What should be ideal time for equibrating the protein with solvent ? How should it be determined, or it is based on experimenting with different conditions ? Please help. Regards. -- Sonali Dhindwal -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php -Inline Attachment Follows- -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] Re: ffcharmm27 for HEME
On 15/04/2010 7:11 PM, Ramachandran G wrote: Hello Par: Using the latest git i could able to work on my oxy-hemoglobin system with new gromacs version 4.0.5 successfully. But since my new gromacs version was not installed in parallel i tried using older version of gromacs 3.3.1 which was installed in parrallel. While doing grompp to get the *.tpr file, i am getting the below error. - Program grompp, VERSION 3.3.1 Source code file: topdirs.c, line: 103 Fatal error: Invalid dihedral type 9 -- Don't bother with 3.3.1 at all, and don't install 4.0.5 (which has had many bugs fixed in 4.0.7). Just wait for 4.0.7 to be installed. Firstly, you have the above compatibility problem. Secondarily, the way parallel simulations are managed has changed significantly. Search the GROMACS webpage for discussion here. Mark I am planning to install the newer gromacs version also in parallel but in the mean time i also wanted to rectify the above error, if i can. Thank you. Rama On Thu, Mar 18, 2010 at 3:02 AM, Pär Bjelkmar mailto:bjelk...@cbr.su.se>> wrote: Hi, I have now added the charmm files to git head and the protein and lipid parts should work at least. Simply check out the latest git and the charmm parameters should show up in pdb2gmx. /Pär 11 mar 2010 kl. 03.04 skrev Ramachandran G: Hello Bjelkumar, Thanks for your reply. I will wait until you add the new force field to the git. regards, rama On Tue, Mar 2, 2010 at 12:47 AM, Pär Bjelkmar mailto:bjelk...@cbr.su.se>> wrote: Hello, I have that on my schedule for next week. That is to add the new force field format to the git source code tree. Until then you could use the old format if you checkout a previous version of the source code. I guess you know about git otherwise there's some info here http://www.gromacs.org/Developer_Zone/Git/Basic_Git_Usage So start by getting a copy of the latest _developing_ version (git head) of gromacs source code: $ git clone g...@git.gromacs.org:gromacs.git The force field files were update in end of January to you could checkout a version from Jan 27 by: $ git checkout d80138d720fd41a5005238adecd5bfd5400e524c then compile. Now it should work if you got the HEME parameters from Michel. Alternatively you wait until end of next week when I think I have had time to add the new force field format to the git head. Good luck! /Pär 1 mar 2010 kl. 21.21 skrev Ramachandran G: Dear Pär Bjelkmar, After getting help from Michel Cuendet still i am facing problem and i understood that in groamcs latest version 4.0.x problems may come due to CMAP. He suggested me to seek your help. Could you help me to get new toplogy format charmm files which can adapt the HEME sections to that. Thank you. Rama -- Forwarded message -- From: *Michel Cuendet* mailto:michel.cuen...@isb-sib.ch>> Date: Fri, Feb 26, 2010 at 1:03 PM Subject: Re: ffcharmm27 for HEME To: Ramachandran G mailto:gtr...@gmail.com>> Dear Mr. Ramachandran, This means you are using grompp from the distribution version 4.0.x. This version of gromacs does not know about the CMAP forcefield term. You have two options : 1) Deactivate CMAP. This would be equivalent to using the charmm22 ff instead of the charmm27, which many people consider fine. To do this, edit the file ffcharmm27.rtp and delete all [cmap] sections. This _should_ work. 2) Download the git development version, which knows how to handle CMAP. I know they have been changing topology formats in the latest versions, but I hope it is still able to read the old topologies. Otherwise, you will have to ask Par Bjelkmar for the charmm files in the new topology format, and adapt the HEME sections to that. Sorry it is a bit messy at the moment. But everything should become part of the gormacs4.1 distribution. Bye, Michel Ramachandran G wrote: > Dear Mr. Michel, > Thank you very much for you help and time. > Although i could able to do pdb2gmx and get the *.top file still, i > have problem in getting the 'tpr' file using grompp. This is due the > 'cmap' > > I would try to fix the problem myself but still if the problem persist > then i will get b
[gmx-users] Re: ffcharmm27 for HEME
Hello Par: Using the latest git i could able to work on my oxy-hemoglobin system with new gromacs version 4.0.5 successfully. But since my new gromacs version was not installed in parallel i tried using older version of gromacs 3.3.1 which was installed in parrallel. While doing grompp to get the *.tpr file, i am getting the below error. - Program grompp, VERSION 3.3.1 Source code file: topdirs.c, line: 103 Fatal error: Invalid dihedral type 9 -- I am planning to install the newer gromacs version also in parallel but in the mean time i also wanted to rectify the above error, if i can. Thank you. Rama On Thu, Mar 18, 2010 at 3:02 AM, Pär Bjelkmar wrote: > Hi, > > I have now added the charmm files to git head and the protein and lipid > parts should work at least. Simply check out the latest git and the charmm > parameters should show up in pdb2gmx. > > /Pär > > 11 mar 2010 kl. 03.04 skrev Ramachandran G: > > Hello Bjelkumar, > Thanks for your reply. I will wait until you add the new force > field to the git. > > regards, > rama > > On Tue, Mar 2, 2010 at 12:47 AM, Pär Bjelkmar wrote: > >> Hello, >> >> I have that on my schedule for next week. That is to add the new force >> field format to the git source code tree. Until then you could use the old >> format if you checkout a previous version of the source code. I guess you >> know about git otherwise there's some info here >> http://www.gromacs.org/Developer_Zone/Git/Basic_Git_Usage >> >> So start by getting a copy of the latest _developing_ version (git head) >> of gromacs source code: >> $ git clone g...@git.gromacs.org:gromacs.git >> The force field files were update in end of January to you could checkout >> a version from Jan 27 by: >> $ git checkout d80138d720fd41a5005238adecd5bfd5400e524c >> >> then compile. Now it should work if you got the HEME parameters from >> Michel. Alternatively you wait until end of next week when I think I have >> had time to add the new force field format to the git head. >> >> Good luck! >> /Pär >> >> 1 mar 2010 kl. 21.21 skrev Ramachandran G: >> >> Dear Pär Bjelkmar, >> After getting help from Michel Cuendet still i am facing problem >> and i >> understood that in groamcs latest version 4.0.x problems may come due to >> CMAP. >> He suggested me to seek your help. Could you help me to get new toplogy >> format charmm files which can adapt the HEME sections to that. >> Thank you. >> >> Rama >> >> -- Forwarded message -- >> From: Michel Cuendet >> Date: Fri, Feb 26, 2010 at 1:03 PM >> Subject: Re: ffcharmm27 for HEME >> To: Ramachandran G >> >> >> >> Dear Mr. Ramachandran, >> >> This means you are using grompp from the distribution version 4.0.x. >> This version of gromacs does not know about the CMAP forcefield term. >> You have two options : >> >> 1) Deactivate CMAP. This would be equivalent to using the charmm22 ff >> instead of the charmm27, which many people consider fine. To do this, >> edit the file ffcharmm27.rtp and delete all [cmap] sections. This >> _should_ work. >> >> 2) Download the git development version, which knows how to handle CMAP. >> I know they have been changing topology formats in the latest versions, >> but I hope it is still able to read the old topologies. Otherwise, you >> will have to ask Par Bjelkmar for the charmm files in the new topology >> format, and adapt the HEME sections to that. >> >> Sorry it is a bit messy at the moment. But everything should become part >> of the gormacs4.1 distribution. >> >> Bye, >> Michel >> >> Ramachandran G wrote: >> > Dear Mr. Michel, >> > Thank you very much for you help and time. >> > Although i could able to do pdb2gmx and get the *.top file still, i >> > have problem in getting the 'tpr' file using grompp. This is due the >> > 'cmap' >> > >> > I would try to fix the problem myself but still if the problem persist >> > then i will get back to you. Thank you again. >> > >> > regards, >> > Rama >> > >> > On Thu, Feb 25, 2010 at 8:59 AM, Michel Cuendet >> > mailto:michel.cuen...@isb-sib.ch>> wrote: >> > >> > >> > Dear Mr. Ramachandran, >> > >> > Attached is a tar file containing the ffcharmm27 forcefield files >> > modified for the HEME and an optional CO ligand. >> > >> > Note that I also wanted to add the O2 ligand, but the original >> charmm >> > parameters seem to be inconsistent. For example, the FE-OM-OM angle >> is >> > 180deg, which is wrong. And there is no angle defined for NH2-FE-OM, >> > while a strong angle is required to keep the ligands axial. So we >> have >> > corrected this and guessed a couple of missing parameters for our >> own >> > use. But I do not include them to the official ffcharmm27 >> > distribution, >> > which should stay as close as pos
Re: [gmx-users] Time for equilibration
Thanks for the answer, My protein strucutre is a homology model,,on which i want to do the simulation. and the change in conformation after MD simulation is more than RMSD of 2 Angstrom, that too in the active site of the protein and you said that "Using position restrain on the heavy atoms of the protein first, and then on the Calphas is generally a goodidea." How we can do this ?? and you also mentioned that time period could b increased from 100 to 500 ps, does increase in time will be helpful in not distorting the strucutre ? Regards -- Sonali Dhindwal --- On Thu, 15/4/10, XAvier Periole wrote: From: XAvier Periole Subject: Re: [gmx-users] Time for equilibration To: "Discussion list for GROMACS users" Date: Thursday, 15 April, 2010, 1:46 PM The distortion of a protein starting structure can result from various reasons:1- experimental determination of the structure: this include the experimentalconditions (T, pH) as well as the crystal contacts if X-ray were used, dynamicsof some part of the molecule if NMR.2- the manner you solvate and equilibrate. Using position restrain on the heavy atoms of the protein first, and then on the Calphas is generally a goodidea. The time you need to run those simulations depends on the system. Ifyou see deviations you can try to run a bit longer. 100 ps is generally sufficientbut can be extended to 500 ps, this is no problem.3- the force field you are using might also trigger some "small" deviations of the protein. The protein structure might contain "strange" local configuration thatare not sable in the FF. 4- you set up, meaning time step, temperature, pressure, ... Note finally that a deviation from the starting structure might just be a fluctuationof a labile region of the protein ... On Apr 15, 2010, at 8:40 AM, sonali dhindwal wrote: Hello All, I have a protein of 576 amino acid long, and has a barell shape topolgy. I have done MD simulation on it for 1ns, and my protein has got distorted shape, i.e, one of the strand became coil and other strands became small. I wrote this query before also, can it be possible that this is due to equilibration conditons i am giving, i am equilibrating it for 100 ps under NVT using brendenson coupling. What should be ideal time for equibrating the protein with solvent ? How should it be determined, or it is based on experimenting with different conditions ? Please help. Regards. -- Sonali Dhindwal -- gmx-users mailing list gmx-us...@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php -Inline Attachment Follows- -- gmx-users mailing list gmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] How to remove overlapping lipid residues?
There are gmx tools that explicitly do this. Either you determine which lipid to remove using a visualization tool like VMD and remove the lipids by editing the gro/pdb file, either you use on of the tools associated with gmx to insert a protein a membrane bilayer. on the gmx tutorials: http://www.gromacs.org/Documentation/How-tos/Membrane_Simulations one from G. Groenhof group: http://wwwuser.gwdg.de/~ggroenh/membed.html On Apr 15, 2010, at 9:32 AM, Jignesh Patel wrote: Hello, Can anyone tell me how to remove overlapping lipid residues? Thanking you. -- Best Wishes, Jignesh Patel Pharmacoinformatics, NIPER -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] Time for equilibration
The distortion of a protein starting structure can result from various reasons: 1- experimental determination of the structure: this include the experimental conditions (T, pH) as well as the crystal contacts if X-ray were used, dynamics of some part of the molecule if NMR. 2- the manner you solvate and equilibrate. Using position restrain on the heavy atoms of the protein first, and then on the Calphas is generally a good idea. The time you need to run those simulations depends on the system. If you see deviations you can try to run a bit longer. 100 ps is generally sufficient but can be extended to 500 ps, this is no problem. 3- the force field you are using might also trigger some "small" deviations of the protein. The protein structure might contain "strange" local configuration that are not sable in the FF. 4- you set up, meaning time step, temperature, pressure, ... Note finally that a deviation from the starting structure might just be a fluctuation of a labile region of the protein ... On Apr 15, 2010, at 8:40 AM, sonali dhindwal wrote: Hello All, I have a protein of 576 amino acid long, and has a barell shape topolgy. I have done MD simulation on it for 1ns, and my protein has got distorted shape, i.e, one of the strand became coil and other strands became small. I wrote this query before also, can it be possible that this is due to equilibration conditons i am giving, i am equilibrating it for 100 ps under NVT using brendenson coupling. What should be ideal time for equibrating the protein with solvent ? How should it be determined, or it is based on experimenting with different conditions ? Please help. Regards. -- Sonali Dhindwal -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] how to calculate diffusion constant of the entire lipid-bilayer
On Apr 15, 2010, at 3:05 AM, Sanku M wrote: Hi, I was interested in calculating the diffusion constant of the center of mass of entire lipid-bilayer ( not individual lipid molecules). Regarding this, I had two doubts I wanted to clarify: 1. Since I am interested in calculating the diffusion constant of the bilayer iteself, I guess I should allow the drift of the bilayer and hence not then remove the center of mass motion of bilayer (and solvent ) separately. Is that right ? If so, is it still OK to remove the center of mass of whole system ( bilayer + water together ) ? 2. How to calculate the mean square displacement of center of mass of the entire bilayer. I guess, g_msd program by default, calculate the diffusion constant of the individual atoms or molecules.But, is there a way to get the diffusion constant of the entire bilayer center of mass ? If I specify the index group which consist of all the atoms of the bilayer, will g_msd provide the diffusion constant of its center of mass or it will give the diffusion constant of individual atoms ? I guess, in that case, one should not use -rmcomm option . Is that right ? You are right. use g_rms with the lipid bilayer as a group. And removing the COM motion during the simulation is what you want to do. The question to answer is: is that meaningful? You probably know what you re doing. Thanks Jagannath -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] How to remove overlapping lipid residues?
Hello, Can anyone tell me how to remove overlapping lipid residues? Thanking you. -- Best Wishes, Jignesh Patel Pharmacoinformatics, NIPER -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
